RetrogeneDB ID: | retro_cjac_3275 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 9:20025690..20026696(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | EGLN2 | ||
| Ensembl ID: | ENSCJAG00000014887 | ||
| Aliases: | None | ||
| Description: | egl nine homolog 2 (C. elegans) [Source:HGNC Symbol;Acc:14660] |
Retrocopy-Parental alignment summary:
>retro_cjac_3275
GACAGCCTGTGCCAGCCGCAGCCCCTAAGTCAGGCTCTCCCTCAGTTACCGGGGTCTTCGTCAGAGCCCTTGGAGCCTGG
CCGGGCCAGGATGGGGGTGGAGAGTTACCTGCCCTGTCCCTTGCTCCCCTCCTACCACTGTCCAGGAGTGCCCAGTGAGG
CCTCGGCAGGGAGTGGGACCCCCAGAGCCACAGCCACCTCTGCCATTGCCAGCCCCCTTCGGGAGGGCTTTGGTGGGCAG
GATGGTGGTGAGTTGTGGCTGCTGCAGAGTGAAGGTGCCGCGCTGGTCACCAAGGGGTGCCAGTGACTGGCAGCCCAGGA
TTCCCGGCCTGAAGCCCCCAAACGGAAATGGGCCGAGGATAGTGGGGATGCCCCTTCACCCAGCAAGCGGCCCTGGGCCA
GGCAAGAGAACCAGGAGGTAGAGCAGTGGGAGGGTGGTATGAGCTGAGGCTGCAGCAGTGGCAGTGGTGAGGCCAGCGCT
GGGCTGACGGAGGAGGTGCTGCCCTGTGCGCCTGAGCGCCTGGCCCTGGACTATATCGTGCCCTGCATGCGGTACTACGG
CATCTGCGTCCAGGACAGCTTCCTGGGGGCAGCACTGGGTGGCCGCGTGCTGGCCGAGGTGGAGCCCCCTCAAACGGGGT
GGGCGCCTGCGAGATGGGCAGCTGGTCAGCCTGGGGGGATCCCACCGCGCAGCATCCGTGGGGACTAGATTGCCTGGGTG
GAAGGCCATGAGCCAGGCTCCGAAGTATCGGTGCCCTCAGGGCCCATGTGGACGCCGTCATCCGCCACTGCTCAGGGCGG
CGGGCAGCTACGTCATCAATGGGCGCACCAAGGCCGTGGTGGCGTTTCCCAGGCAACGGGCTCGGTACGTAAGTCACGTT
GACAATCCCCATGGTGACATCACCTGTATCTATTACCTGACTCAGAACTGGGGCGTTAAGGTGCATGGAGGCCTGCTGCA
GATCTTCCCTGAGGGCCGGCTGGTGGTAGCCAACATCGAGCCACTC
ORF - retro_cjac_3275 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.9 % |
| Parental protein coverage: | 83.99 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | DSPCQPQPLSQALPQLPGSSSEPLEPGRARMGVESYLPCPLLPSYHCPGVPSEASAGSGTPRATATSTTA |
| DS.CQPQPLSQALPQLPGSSSEPLEPGRARMGVESYLPCPLLPSYHCPGVPSEASAGSGTPRATATS..A | |
| Retrocopy | DSLCQPQPLSQALPQLPGSSSEPLEPGRARMGVESYLPCPLLPSYHCPGVPSEASAGSGTPRATATSAIA |
| Parental | SPLREGFGGQDGGELRPLQSEGAAALVTKGCQRLAAQGARPEAPKRKWAEDGGDAPPPSKRPWARQENQE |
| SPLREGFGGQDGGEL..LQSEGAA.LVTKGCQ.LAAQ..RPEAPKRKWAED.GDAP.PSKRPWARQENQE | |
| Retrocopy | SPLREGFGGQDGGELWLLQSEGAA-LVTKGCQ*LAAQDSRPEAPKRKWAEDSGDAPSPSKRPWARQENQE |
| Parental | AEQREGGMSCGCSSGSGEASAGLMEEVLPSAPERLALDYIVPCMRYYGICVKDSFLGAALGGRVLAEVE- |
| .EQ.EGGMS.GCSSGSGEASAGL.EEVLP.APERLALDYIVPCMRYYGICV.DSFLGAALGGRVLAEVE. | |
| Retrocopy | VEQWEGGMS*GCSSGSGEASAGLTEEVLPCAPERLALDYIVPCMRYYGICVQDSFLGAALGGRVLAEVE> |
| Parental | ALKRGGRLRDGQLVS-QRAIPPRSIRGDQIAWVEGHEPG-CRSIGALMAHVDAVIRHCAGR-LGSYVING |
| .LKRGGRLRDGQLVS....IPPRSIRGD.IAWVEGHEPG..RSIGAL.AHVDAVIRHC.GR..GSYVING | |
| Retrocopy | PLKRGGRLRDGQLVS<PGGIPPRSIRGD*IAWVEGHEPG<LRSIGALRAHVDAVIRHCSGR<AGSYVING |
| Parental | RTKAMVACYP-GNGLG-YVRHVDNPHGDGRCITCIYYLNQNWDVKVHGGLLQIFPEGRPVVANIEPL |
| RTKA.VA..P.GNGLG.YV.HVDNPHGD...ITCIYYL.QNW.VKVHGGLLQIFPEGR.VVANIEPL | |
| Retrocopy | RTKAVVA-FP>GNGLG<YVSHVDNPHGD---ITCIYYLTQNWGVKVHGGLLQIFPEGRLVVANIEPL |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP051959_colon | 0 .60 RPM | 4 .50 RPM |
| SRP051959_heart | 0 .07 RPM | 8 .84 RPM |
| SRP051959_kidney | 0 .04 RPM | 6 .86 RPM |
| SRP051959_liver | 0 .00 RPM | 3 .29 RPM |
| SRP051959_lung | 0 .07 RPM | 10 .09 RPM |
| SRP051959_lymph_node | 0 .07 RPM | 8 .79 RPM |
| SRP051959_skeletal_muscle | 0 .07 RPM | 5 .74 RPM |
| SRP051959_spleen | 0 .08 RPM | 9 .58 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3275 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3275 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3275 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000005079 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000014887 | 1 retrocopy |
retro_cjac_3275 ,
|
| Felis catus | ENSFCAG00000024463 | 1 retrocopy |